Element Column(s) Description
Basepairs: 1,2 Basepairs (X:Y) represented by nucleotide position numbers in rRNA:
  • E. coli: position numbers in the Escherichia coli rRNA
  • T. therm.: position numbers in the Thermus thermophilus rRNA
  • H. maris.: position numbers in the Haloarcula marismortui rRNA
Conservations: 3,4 Conservations of nucleotides in basepairs:
  • Cons.T: conservations in total domains (three phylogenetic domains (3P) and two organelles (2O))
  • Cons.3: conservations in the three phylogenetic domains (Bacteria, Archaea, and Eukaryotes)
  • Cons.B: conservations in Bacteria
  • Cons.A: conservations in Archaea
bpT: 5 one of the 16 possible basepair types: C:G, G:C, U:A, A:U, U:G, G:U, G:A, A:G, C:A, A:C, U:C, C:U, A:A, C:C, G:G, and U:U.
bpC: 6 basepair conformations based on the Lee-Gutell system (CRW Site Manuscript Page / Figure 1 / JMB 344:1225-1249 (2004)):
  • The crystal structures analyzed:
    • 16S rRNA in the native T. thermophilus 30S structure (PDB 1FJF)
    • 23S rRNA in the native H. marismortui 50S structure (PDB 1FFK)
    • L11-binding region in the revised version of the H. marismortui 50S structure (PDB 1JJ2)
  • Parentheses are used to disambiguate multiple H-bonding possibilities for a basepair conformation or basepair conformations with bifurcated H-bonds.
    • numbers (1, 2, ...): to disambiguate H-bonding possibilities of a basepair conformation, ex) rS(1), rS(2), rH(1), rH(2), ...
    • bif: to disambiguate basepair conformations with bifurcated hydrogen bonding interactions
  • The two different basepair conformations in 1FFK and 1JJ2 were separated by a slash (/) from each other.
RS: 7 RasMol scripts for displaying all the basepairs in the crystal structures.
Motifs (hatelgkc43uv): 8 basepairs being associated with 13 structural motifs represented with single letter codes:
  • h: secondary structure helices containing at least two basepairs with the canonical basepair conformations, regardless of the basepair types
  • a: AA.AG@helix.ends motifs (JMB 310, 735-753 (2001))
  • t: tandem GA motifs (JMB 242, 1-8 (1994); Biochem 29, 8813-8819 (1990))
  • e: E loop motifs (Biochem 32, 1078-1087 (1993); Nat Str Biol 1, 820-827 (1994); JMB 283, 571-583 (1998); Jung Lee, Dissertation (2003))
  • l: E-like loop motifs (Jung Lee, Dissertation (2003); JMB 304, 335-354 (2000))
  • g: GGA/GAA motifs (Jung Lee, Dissertation (2003); Biochem 44, 2845-2856 (2005))
  • k: K-turn motifs (EMBO J 20, 4214-4221 (2001))
  • c: C-loop motifs (NAR 33, 2395-2409 (2005))
  • 4: tetraloops (G for GNRA, U for UNCG, and C for CUUG)
    • red (G, U, C): tetraloops with tertiary interactions
    • green (G, U, C): tetraloop motifs with no tertiary interactions
    • blue (G, U, C): basepairs with which tetraloop nucleotides interact
  • 3: lonepair triloop motifs (JMB 325, 65-83 (2003))
  • u: UAA/GAA motifs (manuscript in preparation)
  • v: Lone U:A basepair motifs at helix ends (manuscript in preparation)
BT: 9 base triple interactions between a basepair and a third unpaired nucleotide:
  • (X:Y)Z representing base-base interactions between a basepair and a third nucleotide
  • (X:Y).Z representing base-backbone interactions between a basepair and a third nucleotide
BQ: 10 base quadruple interactions between two basepairs:
  • (X:Y)|(M:N) represents base-base interactions between two basepairs
  • (X:Y).(M:N) represents either base-backbone interactions between two basepairs